The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem

Inskeep, William P.

doi:10.3389/fmicb.2013.00067

Cited by 178 publications

(249 citation statements)

References 52 publications

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“…Faster analysis can be obtained with the Illumina MiSeq instrument. However, despite there is evidence that the MiSeq offers valuable information for shotgun sequencing and can Rev Environ Sci Biotechnol (2017) 16:425-454 431 Table 1 State-of-the-art of the microbial metagenomics in geothermal environments worldwide Crenarchaeota (Sulfolobales) (Inskeep et al 2010) (Inskeep et al 2013a) (Inskeep et al 2013b) (Menzel et al 2015) 14 NL 58…”

Section: Next Generation Sequencing Technologymentioning

confidence: 99%

“…1) usually produce millions of short sequence reads up to 800 bp. To date, the most used sequencing techniques are Roche 454 and Illumina that have now been extensively applied to metagenomic from geothermal environments (Inskeep et al 2013b;Menzel et al 2015) (Table 1).…”

Section: Next Generation Sequencing Technologymentioning

confidence: 99%

“…Crenarchaeota (Sulfolobales) (Inskeep et al 2013a) (Inskeep et al 2013b) (Menzel et al 2015) (Bolduc et al 2012) 15 MG N.R.…”

Section: Low Concentration Of Dissolved Oxygen and Sulfidementioning

confidence: 99%

“…Presence of sulfur sediments Crenarchaeota (Desulfurococcales, Thermoproteales) (Inskeep et al 2013a) (Inskeep et al 2013b) 16 CIS Crenarchaeota (Desulfurococcales, Thermoproteales) (Inskeep et al 2013a) (Inskeep et al 2013b) be used to test-run sequencing libraries before analysis on HiSeq instruments, deeper sequencing is strictly required in order to detect the majority of species in a sample and to perform an high quality assembly with a good abundance estimation of the microorganisms (Clooney et al 2016).…”

Section: Nr Low Dissolved Oxygen Concentrationmentioning

confidence: 99%

“…To date, the widest investigation of microbial communities in hyperthermophilic environments (known as the YNP metagenome project) spans over 20 different geothermal sites in the YNP, 13 of which showing temperatures above 65°C. These sites have been pooled in two different ecosystems based on features such as pH, temperature, presence of dissolved sulfide and elemental sulfur that are the main determinants shaping the microbiome within (Inskeep et al 2013b). The first ecosystem, populated by Aquificales-rich ''filamentous-streamer'' communities, was identified in six sites: Dragon Spring (DS; 68-72°C, pH 3.1); 100 Spring Plan (OSP_14; 72-74°C, pH 3.5), Octopus Spring (OS; 74-76°C, pH 7.9) and Bechler Spring (BCH; 80-82°C, pH 7.8) together with MHS and CS described above (Inskeep et al 2013b;TakacsVesbach et al 2013).…”

Section: Yellowstone National Park Usamentioning

confidence: 99%

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Metagenomics of microbial and viral life in terrestrial geothermal environments

Strazzulli

Fusco

Cobucci‐Ponzano

et al. 2017

Rev Environ Sci Biotechnol

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Geothermally heated regions of Earth, such as terrestrial volcanic areas (fumaroles, hot springs, and geysers) and deep-sea hydrothermal vents, represent a variety of different environments populated by extremophilic archaeal and bacterial microorganisms. Since most of these microbes thriving in such harsh biotopes, they are often recalcitrant to cultivation; therefore, ecological, physiological and phylogenetic studies of these microbial populations have been hampered for a long time. More recently, culture-independent methodologies coupled with the fast development of next generation sequencing technologies as well as with the continuous advances in computational biology, have allowed the production of large amounts of metagenomic data. Specifically, these approaches have assessed the phylogenetic composition and functional potential of microbial consortia thriving within these habitats, shedding light on how extreme physico-chemical conditions and biological interactions have shaped such microbial communities. Metagenomics allowed to better understand that the exposure to an extreme range of selective pressures in such severe environments, accounts for genomic flexibility and metabolic versatility of microbial and viral communities, and makes extreme-and hyper-thermophiles suitable for bioprospecting purposes, representing an interesting source for novel thermostable proteins that can be potentially used in several industrial processes.Keywords Hyperthermophiles Á Geothermal environments Á Microbial and viral metagenomics Á CRISPR Á Enzyme discovery BackgroundHot springs populated by extreme thermophiles (T opt : 65-79°C) and hyperthermophiles (T opt [ 80°C) (DeCastro et al. 2016) are very diverse and some of them show combinations of extreme chemo-physical conditions, such as temperature, acidic or alkaline pHs, high pressure, and high concentrations of salts and heavy metals (López-López et al. 2013). As with all studies of environmental microbiology, our understanding of the composition, functional and physiological dynamics, and evolution of extreme-and hyper-thermophilic microbial consortia has lagged A. Strazzulli Á M. Moracci Á P. Contursi

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Section: Next Generation Sequencing Technologymentioning

confidence: 99%

Section: Next Generation Sequencing Technologymentioning

confidence: 99%

“…Crenarchaeota (Sulfolobales) (Inskeep et al 2013a) (Inskeep et al 2013b) (Menzel et al 2015) (Bolduc et al 2012) 15 MG N.R.…”

Section: Low Concentration Of Dissolved Oxygen and Sulfidementioning

confidence: 99%

Section: Nr Low Dissolved Oxygen Concentrationmentioning

confidence: 99%

Section: Yellowstone National Park Usamentioning

confidence: 99%

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Metagenomics of microbial and viral life in terrestrial geothermal environments

Strazzulli

Fusco

Cobucci‐Ponzano

et al. 2017

Rev Environ Sci Biotechnol

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The metagenomic landscape of a high‐altitude geothermal spring in Tajikistan reveals a novel Desulfurococcaceae member, Zestomicrobium tamdykulense gen. nov., sp. nov

Dzhuraeva,

Bobodzhanova,

Birkeland

2024

MicrobiologyOpen

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Metagenomic analysis was conducted to assess the microbial community in the high‐altitude Tamdykul geothermal spring in Tajikistan. This analysis yielded six high‐quality bins from the members of Thermaceae, Aquificaceae, and Halothiobacillaceae, with a 41.2%, 19.7%, and 18.1% share in the total metagenome, respectively. Minor components included Schleiferia thermophila (1.6%) and members of the archaeal taxa Pyrobaculum (1.2%) and Desulfurococcaceae (0.7%). Further analysis of the metagenome‐assembled genome (MAG) from the Desulfurococcaceae family (MAG002) revealed novel taxonomy with only 80.95% closest placement average nucleotide identity value to its most closely related member of the Desulfurococcaceae family, which is part of the Thermoproteota phylum comprising hyperthermophilic members widespread in geothermal environments. MAG002 consisted of 1.3 Mbp, distributed into 48 contigs with 1504 predicted coding sequences, had an average GC content of 41.3%, a completeness and contamination rate of 98.7% and 2.6%, respectively, and branched phylogenetically between the Ignisphaera and Zestosphaera lineages. Digital DNA‐DNA hybridization values compared with Ignisphaera aggregans and Zestosphaera tikiterensis were 33.7% and 19.4%, respectively, suggesting that this MAG represented a novel species and genus. Its 16S rRNA gene contained a large 421 bp intron. It encodes a complete gluconeogenesis pathway involving a bifunctional fructose‐1,6‐bisphosphate phosphatase/aldolase; however, the glycolysis pathway is incomplete. The ribulose monophosphate pathway enzymes could be used for pentose synthesis. MAG002 encodes several hydrogen‐evolving hydrogenases, with possible roles as hydrogen sinks during fermentation. We propose the name Zestomicrobium tamdykulense gen. nov. sp. nov. for this organism; it is the first thermophilic genome reported from Tajikistan.

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The influence of temperature and pH on bacterial community composition of microbial mats in hot springs from Costa Rica

et al. 2019

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We used the 16S rRNA gene pyrosequencing approach to investigate the microbial diversity and community composition in several Costa Rican hot springs alongside the latitudinal axis of the country, with a range of temperatures (37–63°C), pH (6–7.5) and other geochemical conditions. A principal component analyses of the physicochemical parameters showed the samples were separated into three geochemically distinct habitats associated with the location (North, Central, and South). Cyanobacteria and Chloroflexi comprised 93% of the classified community, the former being the most abundant phylum in all samples except for Rocas Calientes 1, (63°C, pH 6), where Chloroflexi and Deinococcus‐Thermus represented 84% of the OTUs. Chloroflexi were more abundant as temperature increased. Proteobacteria, Bacteriodetes and Deinococcus‐Thermus comprised 5% of the OTUs represented. Other Phyla were present in very small percentages (<1%). A LINKTREE analysis showed that the community structure of the mats was shaped primarily by pH, separating samples with pH > 6.6 from samples with pH < 6.4. Thus, both pH and temperature were relevant for community composition even within the moderate ranges of variables studied. These results provide a basis for an understanding of the physicochemical influences in moderately thermophilic microbial mats.

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The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem

Cited by 178 publications

References 52 publications

Metagenomics of microbial and viral life in terrestrial geothermal environments

Metagenomics of microbial and viral life in terrestrial geothermal environments

The metagenomic landscape of a high‐altitude geothermal spring in Tajikistan reveals a novel Desulfurococcaceae member, Zestomicrobium tamdykulense gen. nov., sp. nov

The influence of temperature and pH on bacterial community composition of microbial mats in hot springs from Costa Rica

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